Most of the directories are where Maya stores it's internal data caches, maps and what not. The ones you use are

Sourceimages = textures
images = rendered images and data from the artisan tools
Movies = a place to store playblasts
Data = a place to store obj's and scene data you want to keep separate from Maya scenes
scenes = a place to store your ma / mb files

Note Maya wont care if you store your stuff in other places it will simply make organisation more difficult for you and the people working for you. Maya will care if you have no project folder and you try and use the paint tools or you try and cache an animation or do somthing else that causes maya to want to save files.

Hope that helps